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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaacatctgcacttctggtaatgatatataaaactgatagctgatgttgccctttttttctcag

Basic information

species Zea mays
transcript GRMZM2G126517_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126517_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g39420.2 (Oryza sativa), 5'ss of exon 9
TTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtc----------aacatctgcact--------------tctg-gta---atgatat--ataaaactgatagctgatg-ttgccctttttttctcag
| || ||||||||| | ||||| || ||||| |||||| | |||||| ||||||| ||   |||||||||||||||||||| ||| || || || |||| |||  |||          | |  |||| ||              |||| |||    |||||   | | || ||||| || |||  |  |  | || | ||||
TAGGATCTGGGATTTTGATTGCTGTGCCGATTCCCAAGGAACATGCAGCTTCAGGAAATGCTATAGAGTCTGCAATACAGAAAGCCCTCAAGGAAGCAGAgtattgtccttactcccaacctcctgctctctcactttatcttttctgtgtatttgtgatactaacagaaatgatatctaatgactttctatgttgtttcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67038503|gb|CO464823.1|CO464823
EST:     AGGGNAAAAT-ATANAGTCTGNCA-TACAGACAGCTCTAAAAGAGGCAAG                         GGATAAA-GGATAATAGGAA-TGCGATC-CTCCCTTC-TGCTTGAA-GAGT
genomic: AGGG-AAAATTATAGAGTCTG-CAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|60347683|gb|DN214656.1|DN214656
EST:     TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|211233176|gb|FL456644.1|FL456644
EST:     TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|8516322|gb|BE123048.1|BE123048
EST:     AAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: AAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|71533571|gb|DR784330.1|DR784330
EST:     TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|71764026|gb|DR961963.1|DR961963
EST:     TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|211233175|gb|FL456643.1|FL456643
EST:     TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTBTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|88748923|gb|DY533064.1|DY533064
EST:     TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|74236391|gb|DT644305.1|DT644305
EST:     TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|149082842|gb|EE172068.2|EE172068
EST:     TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|31355559|gb|CD439916.1|CD439916
EST:     TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGG                         GGGATAAA-GGATAATAAGAAATGCGATCACTCCCTTCATGCTTGA
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGG-ATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGA
EST: gi|71764027|gb|DR961964.1|DR961964
EST:     TCAGGGAAAATTATAGAGTCTGCTATACAGACAGCTCTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
EST: gi|211420627|gb|FL480892.1|FL480892
EST:     TCAGGGHAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGG                         GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT
genomic: TCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

TTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 128

TTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

TTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 30

TTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaa ... tttttctcagGGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACAGACAGCTCTAAAAGAGGCAGGgtacagtcaacatctgcacttctggtaatgatatataaaactgatagctgatgttgccctttttttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG